A function to report the smallest tip-to-tip distances in a phylogenetic tree

min_brlen() returns a table of smallest tip-to-tip distances in a phylogenetic tree.

Usage

min_brlen(tree, n = 5, verbose = TRUE)

Arguments

tree: A path to tree file in Newick format, or a phylogenetic tree object of class phylo.
n: Number of distances to report (default = 5).
verbose: Logical of whether to print the result to screen (default = TRUE).

Value

an object of class tbl_df

Details

min_brlen() tabulates the smallest tip-to-tip distances in a phylogenetic tree using cophenetic.phylo and prints a table to screen. This is useful when excluding identical or near-identical haplotypes using the '–minbr' parameter in mPTP.

Author

Rupert A. Collins

Examples


# estimate minimum branch length from raxml tree
min_brlen(ape::as.phylo(geophagus_raxml), n = 5)
#> 
#> 
#> ℹ Printing 5 smallest tip-to-tip distances in a tree with 137 tips ...
#> 
#> 
#> |dist     |  n|
#> |:--------|--:|
#> |0.000002 | 12|
#> |0.000003 |  2|
#> |0.000004 |  6|
#> |0.000005 |  2|
#> |0.001561 |  2|